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Thioredoxin peroxidase B from red blood cells

Analyse Thioredoxin peroxidase B from red blood cells in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QMV
Type: protein
Length: 1,970 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin-2
EC: 1.11.1.15
UniProt: P32119
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Peroxiredoxin-2 (EC 1.11.1.15)	protein	197	32% helix, 27% strand	P32119

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.71	0.98	22	empty
2	52	0.71	0.98	19	empty
3	50	0.70	0.98	21	empty
4	277	0.66	0.82	38	empty
5	227	0.64	0.82	34	empty

Interfaces

20 interfaces between chains.

A–B · 2183 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 2144 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2110 Å² buried · 32 hydrogen bonds · protein-protein
I–J · 2104 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 2054 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (nonstandard, oxidation).

Compared structures

1QMV · thioredoxin peroxidase B from red blood cells · the same entry in another collection · chain J against J, TM-score 1.00
P32119 · AlphaFold monomer V2.0 prediction for peroxiredoxin-2 (P32119) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P32119
Elsewhere: RCSB PDB 1QMV · PDBe 1QMV · UniProt P32119

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